Model Internals

Each PhenDB model is trained on sets of bacterial ENOGs (orthologous groups from EggNOG 4.5), which have or have not been identified in the training genomes. Each ENOG is given a weight, with the magnitude of the weight being the importance of that ENOG for the final prediction. The sign of the weight indicates whether the presence (positive weight) or absence (negative weight) of this ENOG is indicative of the trait.

This table lists the 250 highest-ranking ENOGs of this model.

rank in model enog name enog description weight in model
1 ENOG4107T7M Nitrogenase protein alpha chain 0.048551
2 ENOG4108UR2 Nitrogen fixation protein NifX 0.048344
3 ENOG4105CY9 nitrogenase molybdenum-iron protein beta chain 0.044280
4 ENOG4105D0B Nitrogenase protein alpha chain 0.043777
5 ENOG4105DK8 Nitrogenase molybdenum-iron cofactor biosynthesis protein NifN 0.043671
6 ENOG4105XV5 nifz family 0.041266
7 ENOG4105CGC Nitrogenase cofactor biosynthesis protein NifB 0.040974
8 ENOG4107S73 homocitrate synthase 0.039357
9 ENOG4108VQE nitrogen fixation protein 0.033598
10 ENOG4105DSM The key enzymatic reactions in nitrogen fixation are catalyzed by the nitrogenase complex, which has 2 components the iron protein and the molybdenum-iron protein (By similarity) 0.032943
11 ENOG4105WCA Ferredoxin 0.031990
12 ENOG4107WT5 transcriptional regulator (NifA 0.026361
13 ENOG4105PS4 nifq family 0.024179
14 ENOG4105X87 nitrogen fixation 0.020906
15 ENOG4105ND9 Nitrogenase-associated protein 0.020402
16 ENOG4106QR2 NA 0.018874
17 ENOG410605C May protect the nitrogenase Fe-Mo protein from oxidative damage (By similarity) 0.017043
18 ENOG4105E3S small subunit 0.016247
19 ENOG4105ZPS nitrogen fixation protein 0.015255
20 ENOG41084IN nitrogen fixation protein 0.014522
21 ENOG4107RSS Hydrogenase accessory protein HypB 0.014006
22 ENOG4105C8H hydrogenase maturation protein Hypf 0.013896
23 ENOG4107S67 hydrogenase large subunit 0.013442
24 ENOG4105DS4 PAS PAC sensor Signal transduction histidine kinase 0.013243
25 ENOG4105CQS hydrogenase expression formation protein HypD 0.012746
26 ENOG41082N3 4fe-4S ferredoxin, iron-sulfur binding domain protein 0.012581
27 ENOG4108QWQ LRV FeS4 cluster domain protein 0.012533
28 ENOG4107IVC 4Fe-4S ferredoxin, iron-sulfur binding 0.012152
29 ENOG4105FZE dinitrogenase iron-molybdenum cofactor biosynthesis 0.012011
30 ENOG4105C45 hydrogenase expression formation protein (HypE) 0.011859
31 ENOG4107XWS modD protein 0.011272
32 ENOG4105EJ7 Catalyzes the reduction of hydroxylamine to form NH(3) and H(2)O (By similarity) 0.010892
33 ENOG4105TUP type ii secretion system -0.010812
34 ENOG4105CA0 peroxidase 0.010781
35 ENOG4108Z45 hydrogenase maturation protease 0.010735
36 ENOG4105R88 May protect the nitrogenase Fe-Mo protein from oxidative damage (By similarity) 0.010641
37 ENOG4107RIU May be involved in the formation or repair of Fe-S clusters present in iron-sulfur proteins (By similarity) 0.010633
38 ENOG4105QAS Iron-sulfur cluster assembly accessory protein 0.010416
39 ENOG4108WFK NA 0.009969
40 ENOG4105UD9 type ii secretion system -0.009958
41 ENOG4105EPH radical SAM domain protein 0.009926
42 ENOG41062BR nitrogen fixation protein 0.009778
43 ENOG4107Z47 Signal transduction histidine kinase 0.009742
44 ENOG41081QJ UBA THIF-type NAD FAD binding 0.009698
45 ENOG4105DPX Hydrogenase, large subunit 0.009593
46 ENOG4105U82 Ferredoxin 0.009522
47 ENOG4107SBX Type I restriction-modification system R subunit 0.009454
48 ENOG4108USZ hydrogenase 0.009404
49 ENOG4108T5A NA 0.009241
50 ENOG4105CJ1 ABC, transporter 0.009185
51 ENOG4108NJZ Sensory box GGDEF EAL domain protein 0.009117
52 ENOG4108TGK Low-potential electron donor to a number of redox enzymes (By similarity) 0.009055
53 ENOG4107GIM Short-chain dehydrogenase reductase Sdr 0.009004
54 ENOG4108S1R peptidylprolyl cis-trans isomerase 0.008900
55 ENOG4105S3T ferredoxin (2Fe-2S) 0.008896
56 ENOG4105CBC glutamate synthase 0.008780
57 ENOG4105WMM Probably plays a role in a hydrogenase nickel cofactor insertion step (By similarity) 0.008752
58 ENOG4105X41 nifz family 0.008411
59 ENOG4105CNW domain protein 0.008395
60 ENOG4105V5Z Iron-sulfur cluster assembly accessory protein 0.008395
61 ENOG4107UGN N-6 DNA Methylase 0.008378
62 ENOG4108KHX Diguanylate cyclase 0.008062
63 ENOG4105C6Y Udp-glucose 6-dehydrogenase 0.007975
64 ENOG4105C52 Atpase, p-type (Transporting), had superfamily, subfamily ic 0.007952
65 ENOG4105VKA DNA Polymerase Beta Domain Protein Region 0.007944
66 ENOG4105DE2 Pilus assembly protein CpaB -0.007939
67 ENOG4105NB0 Iron-sulfur cluster assembly accessory protein 0.007922
68 ENOG4105DYN CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Acts as a dsDNA endonuclease. May be involved in the integration of spacer DNA into the CRISPR cassette (By similarity) 0.007897
69 ENOG41074MP UPF0103 Mediator of ErbB2-driven cell motility-containing protein 0.007877
70 ENOG4108K8Z nad( )--dinitrogen-reductase ADP-d-ribosyltransferase 0.007789
71 ENOG4105EPM Diguanylate phosphodiesterase 0.007783
72 ENOG4107QKF NADH Ubiquinone plastoquinone (Complex I) 0.007764
73 ENOG4107Y8X dienelactone hydrolase -0.007721
74 ENOG4105Y58 protective protein 0.007713
75 ENOG41082PG Ferredoxin 0.007526
76 ENOG4105DVZ (ABC) transporter 0.007523
77 ENOG4105CWG Catalyzes the last two steps in the biosynthesis of 5- methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position (U34) in tRNA. Catalyzes the FAD-dependent demodification of cmnm(5)s(2)U34 to nm(5)s(2)U34, followed by the transfer of a methyl group from S-adenosyl-L-methionine to nm(5)s(2)U34, to form mnm(5)s(2)U34 (By similarity) -0.007514
78 ENOG41060HI Regulatory protein, FmdB family 0.007509
79 ENOG4105C5I Dehydrogenase 0.007470
80 ENOG4105F9Q Hopanoid biosynthesis associated radical SAM protein HpnH 0.007462
81 ENOG4105KM4 Acetyl-CoA carboxylase, biotin carboxyl carrier protein 0.007450
82 ENOG4105EWU Squalene--hopene cyclase 0.007381
83 ENOG4106AXJ AraC family transcriptional regulator 0.007372
84 ENOG4107QTH restriction modification system DNA specificity domain 0.007363
85 ENOG4107QPT Catalyzes the formation of dTDP-glucose, from dTTP and glucose 1-phosphate, as well as its pyrophosphorolysis (By similarity) -0.007348
86 ENOG4105BZF Glycosyl transferase (Group 1 0.007196
87 ENOG4105C4B ABC transporter, permease 0.007167
88 ENOG4105C47 NADH ubiquinone oxidoreductase 20 kda subunit 0.007147
89 ENOG4107R30 NADH dehydrogenase 0.007094
90 ENOG4108R5S membrane 0.007086
91 ENOG4105ET3 Reduction of activated sulfate into sulfite (By similarity) 0.007084
92 ENOG4108QMJ NA 0.007076
93 ENOG41068YD NA 0.007048
94 ENOG4105C11 sulfate adenylyltransferase), subunit 2 0.007036
95 ENOG4105V13 Pyruvate kinase 0.007021
96 ENOG4105CH8 Succinyl-CoA ligase ADP-forming subunit alpha 0.007017
97 ENOG41064JQ nhl repeat containing protein 0.007004
98 ENOG4105DRP amino acid AbC transporter 0.006977
99 ENOG4107SRD 5-methylcytosine restriction system -0.006955
100 ENOG4105C3T may be the GTPase, regulating ATP sulfurylase activity (By similarity) 0.006933
101 ENOG4105NW6 solute symporter protein 0.006925
102 ENOG4105CA3 membrane-bound lytic murein transglycosylase -0.006918
103 ENOG4107QU8 Transferase 0.006884
104 ENOG4105D7H oxidoreductase 0.006880
105 ENOG4108NSF NA 0.006878
106 ENOG4105C3I Nad-dependent epimerase dehydratase 0.006874
107 ENOG4107QZ7 Cellulose synthase catalytic subunit -0.006872
108 ENOG4105CUU Catalyzes the reversible transfer of the terminal phosphate of ATP to form a long-chain polyphosphate (polyP) (By similarity) 0.006835
109 ENOG4105FB2 class II Aldolase -0.006801
110 ENOG4107XEC aspartate racemase 0.006747
111 ENOG4105DB1 molybdopterin oxidoreductase 0.006734
112 ENOG4108ZVM Short-chain dehydrogenase reductase Sdr -0.006723
113 ENOG4105CMV Succinyl-CoA synthetase subunit beta 0.006718
114 ENOG4108UKG had-superfamily hydrolase, subfamily ia, variant -0.006625
115 ENOG41090U8 NA 0.006616
116 ENOG4105C0Y Responsible for the amidation of carboxylic groups at position A and C of either cobyrinic acid or hydrogenobrynic acid. NH(2) groups are provided by glutamine, and one molecule of ATP is hydrogenolyzed for each amidation (By similarity) 0.006499
117 ENOG4106C2U Pathogenesis related protein-like protein 0.006497
118 ENOG4107QZU type I restriction-modification system -0.006468
119 ENOG4108EPX Catalyzes the last two steps in the biosynthesis of 5- methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position (U34) in tRNA. Catalyzes the FAD-dependent demodification of cmnm(5)s(2)U34 to nm(5)s(2)U34, followed by the transfer of a methyl group from S-adenosyl-L-methionine to nm(5)s(2)U34, to form mnm(5)s(2)U34 (By similarity) 0.006437
120 ENOG4105E78 Catalyzes a mechanistically unusual reaction, the ATP- dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA) to form an ureido ring (By similarity) 0.006424
121 ENOG4107QI1 Mate efflux family protein -0.006407
122 ENOG4105F2M alpha beta hydrolase fold-3 domain protein -0.006390
123 ENOG4105DMQ Methyltransferase 0.006370
124 ENOG4105D6T Catalyzes the deamination of 5-methylthioadenosine and S-adenosyl-L-homocysteine into 5-methylthioinosine and S-inosyl-L- homocysteine, respectively. Is also able to deaminate adenosine (By similarity) 0.006368
125 ENOG4107EES Involved in cell wall formation. Catalyzes the final step in the synthesis of UDP-N-acetylmuramoyl-pentapeptide the precursor of murein (By similarity) 0.006356
126 ENOG4105BZW Glycerate kinase 0.006336
127 ENOG4108JJB ABC transporter 0.006325
128 ENOG4105CB3 Required for the thiolation of cytidine in position 32 of tRNA, to form 2-thiocytidine (s(2)C32) (By similarity) -0.006320
129 ENOG4105EXB Urea carboxylase-associated protein 2 0.006313
130 ENOG4105ERH Fumarylacetoacetate hydrolase -0.006298
131 ENOG4105FDK ABC transporter 0.006289
132 ENOG4105D0F Protein of unknown function, DUF482 -0.006278
133 ENOG4105C08 Histidine kinase 0.006270
134 ENOG4105EIG urea carboxylase-associated protein 1 0.006261
135 ENOG4108VSY crispr-associated protein Cas4 0.006247
136 ENOG4105EN2 IstB domain-containing protein ATP-binding protein -0.006246
137 ENOG4105FBQ ATPase associated with various cellular activities aaa_5 -0.006215
138 ENOG4105C38 Glycyl-tRNA synthetase beta subunit -0.006209
139 ENOG4105BZK Transcription regulator that activates transcription by stimulating RNA polymerase (RNAP) recycling in case of stress conditions such as supercoiled DNA or high salt concentrations. Probably acts by releasing the RNAP, when it is trapped or immobilized on tightly supercoiled DNA. Does not activate transcription on linear DNA. Probably not involved in DNA repair (By similarity) 0.006206
140 ENOG4105QD3 NA 0.006202
141 ENOG4105SUM dienelactone hydrolase 0.006178
142 ENOG4105HN0 NA 0.006162
143 ENOG4106IVZ signal transduction Histidine kinase 0.006148
144 ENOG4105X7T Ni Fe-hydrogenase, b-type cytochrome subunit 0.006139
145 ENOG4105GFX Transcriptional regulator 0.006125
146 ENOG4105Q1Z Protein of unknown function (DUF3024) 0.006102
147 ENOG4105DW3 Response regulator receiver modulated metal dependent phosphohydrolase 0.006058
148 ENOG4105EN6 Membrane -0.006050
149 ENOG4108ZG0 Ompa motb domain protein -0.006038
150 ENOG4105D6J arsenicaL-resistance protein 0.006033
151 ENOG4105KXW Ferredoxin 0.006029
152 ENOG4107QS2 Symporter 0.006015
153 ENOG4108UY6 tripartite ATP-independent periplasmic transporter, DctQ component 0.006007
154 ENOG4108NGR Regulatory component of sensory transduction system 0.005983
155 ENOG4105KUS lysozyme -0.005978
156 ENOG4108R3Z Response regulator receiver domain protein -0.005968
157 ENOG4105EJB Short-chain dehydrogenase reductase Sdr 0.005967
158 ENOG4105D4P Coproporphyrinogen iii oxidase 0.005965
159 ENOG4107RBX acriflavin resistance protein 0.005922
160 ENOG4105D95 Oxidoreductase required for the transfer of electrons from pyruvate to flavodoxin (By similarity) 0.005916
161 ENOG4105VGJ Virulence-associated protein 0.005913
162 ENOG4105CHC glucokinase (EC 2.7.1.2) 0.005906
163 ENOG4105CRY pfkb domain protein -0.005894
164 ENOG4107QXV Phosphate transporter -0.005891
165 ENOG4105CAA catalyzes amidations at positions B, D, E, and G on adenosylcobyrinic A,C-diamide. NH(2) groups are provided by glutamine, and one molecule of ATP is hydrogenolyzed for each amidation (By similarity) 0.005886
166 ENOG4105ZXK Dehydrogenase -0.005881
167 ENOG4105S10 periplasmic binding protein 0.005876
168 ENOG4105DV0 amidase (EC 3.5.1.4 0.005875
169 ENOG4105D08 cbs domain and cyclic nucleotide-regulated nucleotidyltransferase 0.005868
170 ENOG4105QG4 Catalyzes the reversible isomerization between hydroxypyruvate and 2-hydroxy-3-oxopropanoate (also termed tartronate semialdehyde) (By similarity) -0.005868
171 ENOG4105FCN von Willebrand factor 0.005855
172 ENOG4108UNH dienelactone hydrolase 0.005849
173 ENOG4105CMI transporter 0.005841
174 ENOG4105NM1 Replication Protein -0.005830
175 ENOG4105PUF Ferredoxin, 2FE-2S 0.005815
176 ENOG4106E82 Cytochrome 0.005813
177 ENOG4108EWI abc transporter atp-binding protein -0.005809
178 ENOG4105CQZ Histidine kinase 0.005804
179 ENOG41062RH NA 0.005804
180 ENOG4105EDR glucose galactose transporter -0.005799
181 ENOG4105CB8 Multifunctional enzyme that catalyzes the SAM-dependent methylation of uroporphyrinogen III at position C-2 and C-7 to form precorrin-2 and then position C-12 or C-18 to form trimethylpyrrocorphin 2. It also catalyzes the conversion of precorrin-2 into siroheme. This reaction consists of the NAD- dependent oxidation of precorrin-2 into sirohydrochlorin and its subsequent ferrochelation into siroheme (By similarity) 0.005782
182 ENOG4107RGH Aldehyde dehydrogenase 0.005781
183 ENOG4105NBK UPF0345 protein 0.005778
184 ENOG41082FZ EamA-like transporter family 0.005767
185 ENOG4107RX7 Glycogen debranching enzyme -0.005760
186 ENOG4106EAD NA 0.005755
187 ENOG4108R93 Hopanoid biosynthesis associated glycosyl transferase protein HpnI 0.005746
188 ENOG4107SPV Sulfatase -0.005746
189 ENOG41080G9 Cdp-alcohol phosphatidyltransferase 0.005746
190 ENOG4107RFA Glycyl-tRNA synthetase beta subunit 0.005740
191 ENOG4105WQV ferredoxin-like protein 0.005735
192 ENOG4105NXJ NA -0.005726
193 ENOG4105VIG Sec-independent protein translocase protein TatC -0.005725
194 ENOG4105DHC Aminoglycoside phosphotransferase 0.005723
195 ENOG4105EK8 von Willebrand factor, type A 0.005714
196 ENOG4105E4R Precorrin-3B C17-methyltransferase 0.005687
197 ENOG4108SGY acetyltransferase -0.005685
198 ENOG4105W6C Protein of unknown function (DUF2892) 0.005680
199 ENOG4108KTQ Methyltransferase 0.005667
200 ENOG4107QMV Part of the ABC transporter complex PstSACB involved in phosphate import (By similarity) 0.005666
201 ENOG4105C13 Site-specific tyrosine recombinase, which acts by catalyzing the cutting and rejoining of the recombining DNA molecules. The XerC-XerD complex is essential to convert dimers of the bacterial chromosome into monomers to permit their segregation at cell division. It also contributes to the segregational stability of plasmids (By similarity) 0.005659
202 ENOG4108JU2 Major facilitator superfamily MFS_1 0.005650
203 ENOG4105I8X Membrane -0.005648
204 ENOG4105EFU Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic sites (AP sites) to produce new 5'-ends that are base-free deoxyribose 5-phosphate residues. It preferentially attacks modified AP sites created by bleomycin and neocarzinostatin (By similarity) 0.005646
205 ENOG4105EYU Glutamine amido-transferase -0.005644
206 ENOG4108RT7 Glycosyl transferase, family 2 -0.005640
207 ENOG4105Y2D Domain of unknown function DUF123 0.005620
208 ENOG41061EV selenium-binding protein YdfZ 0.005618
209 ENOG4105QNF Outer membrane lipoprotein 0.005612
210 ENOG4105M3N prophage protein 0.005610
211 ENOG41086VZ NA -0.005592
212 ENOG4107S5J Periplasmic binding protein 0.005588
213 ENOG4108IMS Pentapeptide repeat 0.005568
214 ENOG4108MG9 hydrogenase 3 maturation protease 0.005562
215 ENOG4105XD5 NADH ubiquinone oxidoreductase, 20 kda subunit 0.005539
216 ENOG4108EDY Chemotaxis sensory transducer 0.005532
217 ENOG4105QGQ ycii-related protein -0.005527
218 ENOG4105C9Q fumarate hydratase class II -0.005526
219 ENOG4105HZ2 Diguanylate cyclase -0.005523
220 ENOG4107RVX amidohydrolase 0.005511
221 ENOG4105CBX hi0933 family -0.005509
222 ENOG4107X17 Peptidase M48 0.005497
223 ENOG4105K5C Phosphonate degradation operons associated HDIG domain protein 0.005492
224 ENOG4106EI2 helix-turn-helix domain protein 0.005483
225 ENOG4108RUT NADP oxidoreductase, coenzyme f420-dependent 0.005467
226 ENOG4105NDF NAD-dependent protein deacetylase which modulates the activities of several enzymes which are inactive in their acetylated form. May also have NAD-dependent lysine demalonylase and desuccinylase activity (By similarity) 0.005456
227 ENOG4108WUH Transcriptional regulator, TetR family 0.005455
228 ENOG4105EM8 binding-protein-dependent transport systems inner membrane Component 0.005451
229 ENOG4107RUP AcrB AcrD AcrF family protein 0.005449
230 ENOG4105N1V MEKHLA domain protein -0.005448
231 ENOG4108R4U Hnh endonuclease -0.005447
232 ENOG4107R4J Chloride channel 0.005444
233 ENOG41063QB ThiamineS Protein 0.005437
234 ENOG4105WRB Hydrogenase assembly chaperone hypC hupF 0.005435
235 ENOG4106492 Is required to sustain N(2)-dependent growth in the presence of low levels of carbon monoxide (CO). Probably acts by protecting the N(2) fixation ability of the nitrogenase complex, which is inactivated in the presence of CO (By similarity) 0.005429
236 ENOG4107E84 Cytochrome c -0.005415
237 ENOG4105EE5 Membrane protein terC -0.005410
238 ENOG4108ZFK Gcn5-related n-acetyltransferase 0.005407
239 ENOG4105C7Z Conserved Protein 0.005404
240 ENOG4107WAK ABC-2 type transporter 0.005395
241 ENOG4105EW9 transcriptional regulator AsnC family 0.005388
242 ENOG4105EHA HipA domain protein 0.005366
243 ENOG4108IPT Naphthoate synthase 0.005362
244 ENOG4108UGV hypoxanthine phosphoribosyltransferase 0.005350
245 ENOG4105K8D sulfur carrier protein 0.005347
246 ENOG4107R73 Mate efflux family protein 0.005345
247 ENOG4105CGM Catalyzes the phosphorylation of pantothenate (Pan), the first step in CoA biosynthesis (By similarity) 0.005345
248 ENOG4105D0U Arsenite-activated ATPase (ArsA) 0.005345
249 ENOG4105BZM domain protein 0.005342
250 ENOG4105QVV ADP-ribosylglycohydrolase 0.005341